Genomic selection for white spot syndrome virus resistance in whiteleg shrimp boosts survival under an experimental challenge test

Marie Lillehammer,Andres Suarez,Rama Bangera,Nicholas Andrew Robinson,Morten Rye,Marcela Salazar,James Cock,Sergio Vela,Edna C Erazo

doi:10.1038/s41598-020-77580-3

Marie Lillehammer, Andres Suarez + Show 7 more

Open Access

https://doi.org/10.1038/s41598-020-77580-3

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Abstract

White spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The development of resistant shrimp populations is an attractive option for management of the disease. However, heritability for WSSV resistance is generally low and genetic improvement by conventional selection has been slow. This study was designed to determine the power and accuracy of genomic selection to improve WSSV resistance in Litopenaeus vannamei. Shrimp were experimentally challenged with WSSV and resistance was evaluated as dead or alive (DOA) 23 days after infestation. All shrimp in the challenge test were genotyped for 18,643 single nucleotide polymorphisms. Breeding candidates (G0) were ranked on genomic breeding values for WSSV resistance. Two G1 populations were produced, one from G0 breeders with high and the other with low estimated breeding values. A third population was produced from “random” mating of parent stock. The average survival was 25% in the low, 38% in the random and 51% in the high-genomic breeding value groups. Genomic heritability for DOA (0.41 in G1) was high for this type of trait. The realised genetic gain and high heritability clearly demonstrates large potential for further genetic improvement of WSSV resistance in the evaluated L. vannamei population using genomic selection.

Highlights

White spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture
Filtering of the 465,500 putative single nucleotide polymorphisms (SNPs) identified from mRNAseq resulted in 10,323 SNPs (Table S1) which were selected for inclusion in the custom 18 K Illumina SNP array (MAF > 0.1, > 51X coverage and eliminating multiple SNPs per contig and SNP alleles fixed in the R- and susceptible line (S-line))
Estimates of heritability for the dead or alive (DOA) and days survival (DS) traits were similar for the overall G0 population (0.30 for DOA and 0.53 for DS) to those for the pure resistant line (R-line) animals (DOA 0.22 and DS 0.39) and for crossed resistant by susceptible line (RxS) animals (DOA 0.34 and DS 0.48, Table 1)

Summary

Introduction

White spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The realised genetic gain and high heritability clearly demonstrates large potential for further genetic improvement of WSSV resistance in the evaluated L. vannamei population using genomic selection. Disease caused by the White Spot Syndrome Virus (WSSV) is a serious problem for global shrimp aquaculture. It infects all major cultured shrimp species and is highly virulent normally causing death in a few d ays[1]. Estimates of the heritability of WSSV resistance in Litopenaeus vannamei range between 0.01 and 0.31 depending on the batch of shrimp, the trait analysed This gene was mapped to a QTL region on linkage group 43

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